rs2273346
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006610.4(MASP2):āc.1130T>Cā(p.Val377Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 1,613,664 control chromosomes in the GnomAD database, including 2,381 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_006610.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MASP2 | NM_006610.4 | c.1130T>C | p.Val377Ala | missense_variant | 9/11 | ENST00000400897.8 | |
MASP2 | XR_001736931.1 | n.1083T>C | non_coding_transcript_exon_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MASP2 | ENST00000400897.8 | c.1130T>C | p.Val377Ala | missense_variant | 9/11 | 1 | NM_006610.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0600 AC: 9126AN: 152018Hom.: 550 Cov.: 32
GnomAD3 exomes AF: 0.0502 AC: 12612AN: 251006Hom.: 761 AF XY: 0.0504 AC XY: 6844AN XY: 135672
GnomAD4 exome AF: 0.0308 AC: 45045AN: 1461528Hom.: 1830 Cov.: 30 AF XY: 0.0325 AC XY: 23642AN XY: 727080
GnomAD4 genome ? AF: 0.0601 AC: 9148AN: 152136Hom.: 551 Cov.: 32 AF XY: 0.0613 AC XY: 4562AN XY: 74386
ClinVar
Submissions by phenotype
Immunodeficiency due to MASP-2 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at